..Here we further explore the relationship between co-expression and chromosomal co-localization in the human genome by analyzing the expression status of the genes along the best-annotated chromosomes 20, 21 and 22...

..Expression profiles were then generated for each gene by counting their cognate ESTs in all libraries. Differential expression was assessed by applying a previously published statistical procedure to these profiles...

..Their isolation and genome sequencing could prove invaluable in understanding the origin and diversity of large DNA viruses, and shed some light on the role they eventually played in the emergence of eukaryotes...

..We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses...

..Based on previous results and theories on the coding potential of palindromic elements, we speculate that their insertion and mobility might have played a significant role in the early stages of protein evolution...

..It is thus increasingly difficult for the biologist to choose the computational approaches that perform best in these various areas. This paper attempts to review the most useful developments of the last 2 years...

The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite

..An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/...

Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens

..Expression profiles were then generated for each of these genes by counting their cognate ESTs in all libraries. Differential expression was assessed by applying to these profiles a previously published statistical procedure...

..Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought...

..9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study. ..

..In this study, we used a new approach--'phylogenetic mapping'--to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set...

Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes

..Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment...

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

..coli ORFs presently annotated as "hypothetical" correspond to bona fide genes. By extension, this implies that randomly occurring "junk" ORFs have been actively counter selected during the evolution of the dense E. coli genome...

..ii) identify genes expressed in a coordinated manner across a set of conditions; and (iii) delineate clusters of genes sharing coherent expression features, eventually defining global biological pathways...

..The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements...

..The biophysical requirements for the presence of charged residues at the protein surface, allowing protein stabilization through ion bonds, is therefore clearly imprinted and detectable in all genome sequences available to date...

..After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet...

Crystallization and preliminary crystallographic study of a component of the Escherichia coli tol system: TolB

..TolB homologues are found in many gram-negative bacteria and the Tol-PAL system is thought to play a role in bacterial envelope integrity. TolB is required for lethal infection by Salmonella typhimurium in mice...

The structure of Acidithiobacillus ferrooxidans c(4)-cytochrome: a model for complex-induced electron transfer tuning

..and Suzuki, M. (2000) Proc. Natl. Acad. Sci. 97, 14257-14262). We show that the CvP-bias is the sole criterion that is able to clearly discriminate hyperthermophile from mesothermophile microorganisms on a global genomic basis...

..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...